Variant report

Variant	rs10485887
Chromosome Location	chr7:78068055-78068056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11760299	0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs11765817	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs11767605	0.83[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12670044	1.00[YRI][hapmap]
rs13243127	0.83[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs1861384	0.94[EUR][1000 genomes]
rs2110871	0.86[LWK][hapmap]
rs2110873	1.00[YRI][hapmap]
rs34058977	0.94[EUR][1000 genomes]
rs7788384	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10485887	PHTF2	cis	parietal	SCAN
rs10485887	RPL13AP17	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78067000-78068200	Enhancers	Muscle Satellite Cultured Cells	--
2	chr7:78067000-78072400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:78067000-78079800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:78067200-78068400	Enhancers	Fetal Brain Female	brain
5	chr7:78067600-78068400	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr7:78067600-78068800	Enhancers	Brain Hippocampus Middle	brain
7	chr7:78067600-78071600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:78067800-78068200	Enhancers	Psoas Muscle	Psoas
9	chr7:78067800-78068400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr7:78067800-78068400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr7:78067800-78068600	Enhancers	Brain Angular Gyrus	brain
12	chr7:78068000-78068400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr7:78068000-78068600	Enhancers	Brain Substantia Nigra	brain
14	chr7:78068000-78069200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:78068000-78071000	Weak transcription	Brain Anterior Caudate	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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